In my shop, I prefer to charge shipping based on number of items and so I've added a 'weight' to each item and set the shipping up accordingly. It's already a bit contrived and then I add in retail shipping deals and wholesale rates but it seems to work:)
However, I remembered that I had to set up shipping rates in Paypal and those rates are only based on order value. I threw in some basic rates in Paypal but they will not be same as in my shop due to the difference between wholesale and retail pricing.
Do these Paypal rates actually apply to my Shopify sales? I thought that I had to set them up in order to connect Paypal but maybe I am missing something. There is this option in Paypal but I'm not sure if it's relevant to this issue: Click here to allow transaction-based shipping values to override the profile shipping settings listed above (if profile settings are enabled).